The Phantom Virus was the creation of Bill McLemore to try and sabotage a fellow college student's project to win a large amount of money.
It was a glowing form of electrical energy with a seemingly artificial intelligence; mainly blue in color and only clothed for disguise.
The Phantom Virus has an obsession with baseball mirrored by its creator which were the gang's main clues as to who the culprit was. It had the ability to extract data from various electrical devices, as well as control machines and cables. The Virus was however, weak in close proximity to magnets causing agonizing deformation or even the inability to move. It is unknown if Bill could control the Virus or if the Virus recognized Bill as its creator.
Powers and abilities
The Phantom Virus has the ability to steal the network and data from every computer in the world. He was also able to control aspects of Eric's game, for example, the cyber villains that Scooby and the gang faced in the game were all under the control of the virus (however he seemed to be unable to control Mystery Inc.'s cyber counterparts). Another fierce abitlity, he can shoot, well, there's no other aspect, but lightning. In the final level in the movie, he created a giant source of balls flying around all over the place like a tornado and tamper with devices in the arcade making either haywire and shooting balls or punks (sports games) or make them sentient and attack the gang or trap them with wires (regular games).
Scooby-Doo and the Cyber Chase
A laser for transferring material items into the virtual world was also used to extract the Phantom Virus to into the real world of the college campus. There it would wreak havoc and prevent Eric form winning the prize which Bill thought he deserved due to being a longer standing student. Once the gang are accidentally transferred into the game by accident, they compete with the virus who is the "boss" of various monsters in different locations within the game. to defeat the virus,
the gang must find the Scooby Snacks box in each level and progress to the end. the virus has minions in the games such as the two Moon Ghosts, three skeleton gladiators with a lion, a T-Rex, a camel, a dragon, a polar bear, and the five monsters from the past.
In the final level it used the classic monster to hamper the gang and their cyber counterparts, but eventually they made it to the arcade where the final snack book was. When the gang made it there the virus appeared and started making the games go haywire, wrapped up most of the real gang, forcing Scooby to hid,and used the monsters to trap all the gangs counterparts except for Cyber Scooby. At first Cyber Scoob tried to free Fred but Fred came up with a plan to get the box and Cyber Scooby let the still untrap Scoob in on the plan. Cyber Scooby got the viruses attention and kept it busy with the Real Scooby snuck behind him to get the box. The Virus eventually caught Cyber Scoob but was too late to stop the real Scooby, just after he caught him the monster turned around and looked in horror as Scooby secured the box. The minute Scooby picked it up the virus started to become deformed, the arcade went back to normal, and the monster disappeared. The rest of the gang digital counterparts walked in just in time to see the virus disappear from existence forever.